Cardiomyocytes (CMs) derived from human-induced pluripotent stem cells (hiPSCs) are considered a promising platform for multiple applications, including disease modeling, regenerative medicine, screening of drug toxicity and investigation of cardiomyogenesis. Despite remarkable improvement in methodology enabling differentiation of hiPSCs into CMs, applied protocols generate heterogeneous cell populations composed of CMs along with differentiated non-cardiac cell-types and undifferentiated hiPSCs. Here we describea procedure of automated Magnetic-Activated Cell Sorting (autoMACS) for the purification of hiPSCs-derived CMs under sterile culture conditions. We illustrate that this approach led to a robust depletion of non-cardiac cells and enrichment of CMs, a result particularly crucial for hiPSC lines with poor cardiac differentiation efficiencies.